n mix results

N - mixture models by species

modelling N by site to get relative abundance

abundance by site will be used as a cov on predator occupancy

7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ

Species:      AmericanPika

Metadata Summary:

N_sites	N_counts	N_detections	rep_period	iterations	burnin	thin
127	137	59	7 days	120000	20000	10

Detections by Year:

Yr	2016	2017	2018	2019	2020
sites	19	31	19	32	26
detections	5	10	0	24	20
N.dot.model	2	5	0	11	6

WAIC

Models by WAIC:

model	description	WAIC	N.total.est
fm7	counts	3.889332	108
fm4	lure + jdt	358.924599	24
fm2	jdt	359.814351	25
fm6	lure + jdt + jdtSq	360.277323	24
fm5	jdt + jdtSq	360.763399	25
fm3	lure	368.539468	25
fm1	dot	370.195910	24

Model summaries:

model: fm1

dot

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
p[1]	NA	8453	0.131	0.116	0.04	0.21	0	1.0009
p[2]	NA	6013	0.074	0.062	0.03	0.12	0	1.0009
p[3]	NA	10000	0.488	0.272	0.00	0.88	0	0.9843
p[4]	NA	6132	0.060	0.055	0.03	0.09	0	1.001
p[5]	NA	7934	0.127	0.124	0.08	0.17	0	1.001
lambda[1]	NA	8919	0.123	0.066	0.01	0.24	0	0.9932
lambda[2]	NA	4129	0.243	0.169	0.05	0.41	0	1.001
lambda[3]	NA	10000	0.000	err	0.00	0.00	err	err
lambda[4]	NA	5803	0.503	0.423	0.22	0.76	0	1.001
lambda[5]	NA	10000	0.273	0.226	0.09	0.44	0	1.001
N[121]	NA	10092	0.033	err	0.00	0.00	err	err
N[63]	NA	0	0.000	err	0.00	0.00	err	err
N[107]	NA	9373	0.004	err	0.00	0.00	err	err
N[39]	NA	8014	0.073	err	0.00	0.00	err	err
N[88]	NA	9187	0.085	err	0.00	0.00	err	err

p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[121]

N[63]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero

## Warning: Removed 50 rows containing missing values (geom_bar).

N[107]

N[39]

N[88]

model: fm2

jdt

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
alpha	jdt	8406	0.448	0.439	0.22	0.67	0.00618	1.0004
alpha0	NA	6449	-2.611	-2.607	-2.93	-2.29	0	1.001
lambda[1]	NA	10000	0.127	0.07	0.01	0.24	0	0.9939
lambda[2]	NA	10000	0.222	0.17	0.06	0.37	0	1.0008
lambda[3]	NA	10000	0.000	err	0.00	0.00	err	err
lambda[4]	NA	10648	0.417	0.391	0.20	0.62	0	1.001
lambda[5]	NA	9240	0.359	0.294	0.13	0.57	0	1.001
N[105]	NA	9473	0.029	err	0.00	0.00	err	err
N[83]	NA	10107	0.079	err	0.00	0.00	err	err
N[107]	NA	9739	0.028	err	0.00	0.00	err	err
N[101]	NA	8248	0.012	err	0.00	0.00	err	err
N[119]	NA	10000	0.108	err	0.00	0.00	err	err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[105]

N[83]

N[107]

N[101]

N[119]

alpha relationship

model: fm3

lure

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
alpha	lure	10175	-0.113	-0.095	-0.36	0.11	0.76814	0.7752
alpha0	NA	7183	-2.463	-2.45	-2.75	-2.17	0	1.001
lambda[1]	NA	10000	0.131	0.073	0.01	0.25	0	0.9939
lambda[2]	NA	10000	0.206	0.151	0.05	0.34	0	1.0009
lambda[3]	NA	10000	0.000	err	0.00	0.00	err	err
lambda[4]	NA	9188	0.413	0.373	0.19	0.61	0	1.001
lambda[5]	NA	9146	0.330	0.266	0.12	0.53	0	1.001
N[76]	NA	9698	0.078	err	0.00	0.00	err	err
N[55]	NA	0	0.000	err	0.00	0.00	err	err
N[58]	NA	0	0.000	err	0.00	0.00	err	err
N[2]	NA	10000	0.021	err	0.00	0.00	err	err
N[100]	NA	9782	0.015	err	0.00	0.00	err	err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[76]

N[55]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero

## Warning: Removed 50 rows containing missing values (geom_bar).

N[58]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero

## Warning: Removed 50 rows containing missing values (geom_bar).

N[2]

N[100]

alpha relationship

model: fm4

lure + jdt

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
alpha[1]	lureDays	6528	-0.409	-0.421	-0.68	-0.13	0.0605	0.9947
alpha[2]	julianDt	5904	0.615	0.608	0.35	0.86	0	1.001
alpha0	NA	4550	-2.709	-2.705	-3.07	-2.35	0	1.001
lambda[1]	NA	9103	0.117	0.061	0.01	0.23	0	0.9943
lambda[2]	NA	9644	0.204	0.159	0.05	0.34	0	1.0008
lambda[3]	NA	9247	0.000	err	0.00	0.00	err	err
lambda[4]	NA	8955	0.428	0.402	0.21	0.64	0	1.001
lambda[5]	NA	5738	0.473	0.366	0.16	0.77	0	1.001
N[34]	NA	10000	0.019	err	0.00	0.00	err	err
N[125]	NA	10000	0.452	0	0.00	1.00	1	err
N[36]	NA	9284	0.021	err	0.00	0.00	err	err
N[105]	NA	8658	0.105	err	0.00	0.00	err	err
N[14]	NA	8077	0.009	err	0.00	0.00	err	err

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[34]

N[125]

N[36]

N[105]

N[14]

model: fm5

jdt + jdtSq

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
alpha[1]	julianDt	2240	0.212	0.193	-0.21	0.64	0.78346	0.7802
alpha[2]	julianDtSq	2197	0.238	0.253	-0.14	0.60	0.61391	0.8431
alpha0	NA	7177	-2.659	-2.633	-2.97	-2.32	0	1.001
lambda[1]	NA	9696	0.136	0.072	0.01	0.26	0	0.9934
lambda[2]	NA	10650	0.218	0.169	0.06	0.37	0	1.0008
lambda[3]	NA	10000	0.000	err	0.00	0.00	err	err
lambda[4]	NA	10175	0.413	0.376	0.20	0.61	0	1.001
lambda[5]	NA	8986	0.370	0.302	0.14	0.59	0	1.001
N[51]	NA	0	0.000	err	0.00	0.00	err	err
N[18]	NA	10022	0.020	err	0.00	0.00	err	err
N[108]	NA	10000	0.021	err	0.00	0.00	err	err
N[31]	NA	10000	0.014	err	0.00	0.00	err	err
N[59]	NA	0	0.000	err	0.00	0.00	err	err

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[51]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero

## Warning: Removed 50 rows containing missing values (geom_bar).

N[18]

N[108]

N[31]

N[59]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero

## Warning: Removed 50 rows containing missing values (geom_bar).

julian date relationship

model: fm6

lure + jdt + jdtSq

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
alpha[1]	lureDays	6082	-0.402	-0.384	-0.68	-0.11	0.06838	0.9913
alpha[2]	julianDt	2289	0.434	0.349	-0.04	0.87	0.31698	0.9382
alpha[3]	julianDtSq	2288	0.186	0.216	-0.20	0.55	0.71535	0.7844
alpha0	NA	4530	-2.749	-2.738	-3.11	-2.37	0	1.001
lambda[1]	NA	10000	0.123	0.075	0.00	0.23	0	0.994
lambda[2]	NA	9588	0.203	0.149	0.05	0.34	0	1.0008
lambda[3]	NA	10000	0.000	err	0.00	0.00	err	err
lambda[4]	NA	8890	0.422	0.368	0.20	0.62	0	1.001
lambda[5]	NA	5724	0.484	0.355	0.16	0.78	0	1.001
N[97]	NA	10000	0.015	err	0.00	0.00	err	err
N[12]	NA	9555	0.009	err	0.00	0.00	err	err
N[70]	NA	10000	0.234	err	0.00	1.00	err	err
N[49]	NA	10000	0.007	err	0.00	0.00	err	err
N[43]	NA	10000	0.004	err	0.00	0.00	err	err

alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[97]

N[12]

N[70]

N[49]

N[43]

model: fm7

counts

summary table

param	covariate	iters_ef	mean	mode	hdi_89pct_lower	hdi_89pct_upper	bayes_P	pct.density
alpha	counts	8863	6.601	5.766	4.57	8.64	0	1.001
alpha0	NA	9717	-7.644	-7.406	-9.21	-5.96	0	1.001
lambda[1]	NA	4197	0.915	0.518	0.04	1.75	0	0.9931
lambda[2]	NA	4909	0.921	0.647	0.22	1.59	0	1.0007
lambda[3]	NA	1580	0.006	err	0.00	0.00	err	err
lambda[4]	NA	8177	0.974	0.91	0.46	1.46	0	1.001
lambda[5]	NA	6460	0.940	0.757	0.30	1.56	0	1.0009
N[56]	NA	1703	0.005	err	0.00	0.00	err	err
N[15]	NA	7057	0.905	0	0.00	2.00	1	err
N[27]	NA	0	1.000	err	1.00	1.00	err	err
N[35]	NA	7512	0.884	0	0.00	2.00	1	err
N[117]	NA	9099	0.914	0	0.00	2.00	1	err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[56]

N[15]

N[27]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero

## Warning: Removed 50 rows containing missing values (geom_bar).

N[35]

N[117]

alpha relationship